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1. ARF19 Condensation in the Arabidopsis Stomatal Lineage

   Kuan, Chi; Strader, Lucia C.; Morffy, Nicholas (February 2023, microPublication biology)

   The phytohormone auxin regulates nearly every aspect of plant development. Transcriptional responses to auxin are driven by the activities of the AUXIN RESPONSE FACTOR family of transcription factors. ARF19 (AT1G19220) is critical in the auxin signaling pathway and has previously been shown to undergo protein condensation to tune auxin responses in the root. However, ARF19 condensation dynamics in other organs has not yet been described. In the Arabidopsis stomatal lineage, we found that ARF19 cytoplasmic condensates are enriched in guard cells and pavement cells, terminally differentiated cells in the leaf epidermis. This result is consistent with previous studies showing ARF19 condensation in mature root tissues. Our data reveal that the sequestration of ARF19 into cytoplasmic condensation in differentiated leaf epidermal cells is similar to root-specific condensation patterns. 

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2. Generation of a fertile ask1 mutant uncovers a comprehensive set of SCF‐mediated intracellular functions

   https://doi.org/10.1111/tpj.14939  

   Yapa, Madhura M.; Yu, Peifeng; Liao, Fanglei; Moore, Abigail G.; Hua, Zhihua (August 2020, The Plant Journal)

   Summary Many eukaryotic intracellular processes employ protein ubiquitylation by ubiquitin E3 ligases for functional regulation or protein quality control. In plants, the multi‐subunit Skp1–Cullin1–F‐box (SCF) complexes compose the largest group of E3 ligases whose specificity is determined by a diverse array of F‐box proteins. Although both sequence divergence and polymorphism ofF‐boxgenes well support a broad spectrum of SCF functions, experimental evidence is scarce due to the low number of identified SCF substrates. Taking advantage of the bridge role of Skp1 between F‐box and Cullin1 in the complex, we systematically analyzed the functional influence of a well‐characterizedArabidopsis Skp1‐Like1(ASK1)Dsinsertion allele,ask1, in different Arabidopsis accessions. Through 10 generations of backcrossing with Columbia‐0 (Col‐0), we partially rescued the fertility of this otherwise sterileask1allele in Landsbergerecta, thus providing experimental evidence showing the polymorphic roles of SCF complexes. Thisask1mutant produces twisted rosette leaves, a reduced number of petals, fewer viable pollen grains, and larger embryos and seeds compared to Col‐0. RNA‐Seq‐based transcriptome analysis ofask1uncovered a large spectrum of SCF functions, which is greater than a 10‐fold increase compared with previous studies. We also identified its hyposensitive responses to auxin and abscisic acid treatments and enhanced far‐red light/phyA‐mediated photomorphogenesis. Such diverse roles are consistent with the 20–30% reduction of ubiquitylation events inask1estimated by immunoblotting analysis in this work. Collectively, we conclude that ASK1 is a predominant Skp1 protein in Arabidopsis and that the fertileask1mutant allowed us to uncover a comprehensive set of SCF functions. 

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3. Auxin Response Factors promote organogenesis by chromatin-mediated repression of the pluripotency gene SHOOTMERISTEMLESS

   https://doi.org/10.1038/s41467-019-08861-3  

   Chung, Yuhee; Zhu, Yang; Wu, Miin-Feng; Simonini, Sara; Kuhn, Andre; Armenta-Medina, Alma; Jin, Run; Østergaard, Lars; Gillmor, C. Stewart; Wagner, Doris (December 2019, Nature Communications)

   Abstract Specification of new organs from transit amplifying cells is critical for higher eukaryote development. In plants, a central stem cell pool maintained by the pluripotency factor SHOOTMERISTEMLESS (STM), is surrounded by transit amplifying cells competent to respond to auxin hormone maxima by giving rise to new organs. Auxin triggers flower initiation through Auxin Response Factor (ARF) MONOPTEROS (MP) and recruitment of chromatin remodelers to activate genes promoting floral fate. The contribution of gene repression to reproductive primordium initiation is poorly understood. Here we show that downregulation of the STM pluripotency gene promotes initiation of flowers and uncover the mechanism for STM silencing. The ARFs ETTIN (ETT) and ARF4 promote organogenesis at the reproductive shoot apex in parallel with MP via histone-deacetylation mediated transcriptional silencing of STM . ETT and ARF4 directly repress STM , while MP acts indirectly, through its target FILAMENTOUS FLOWER ( FIL ). Our data suggest that – as in animals- downregulation of the pluripotency program is important for organogenesis in plants. 

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4. Conservation and divergence of regulatory architecture in nitrate-responsive plant gene circuits

   https://doi.org/10.1093/plcell/koaf124  

   Bian, Chao; Demirer, Gozde S; Oz, M Tufan; Cai, Yao-Min; Witham, Sam; Mason, G Alex; Di, Zhengao; Deligne, Florian; Zhang, Ping; Shen, Rachel; et al (June 2025, The Plant Cell)

   Abstract Plant roots dynamically respond to nitrogen availability by executing a signaling and transcriptional cascade resulting in altered plant growth that is optimized for nutrient uptake. The NIN-LIKE PROTEIN 7 (NLP7) transcription factor senses nitrogen and, along with its paralog NLP6, partially coordinates transcriptional responses. While the post-translational regulation of NLP6 and NLP7 is well established, their upstream transcriptional regulation remains understudied in Arabidopsis (Arabidopsis thaliana) and other plant species. Here, we dissected a known sub-circuit upstream of NLP6 and NLP7 in Arabidopsis, which was predicted to contain multiple multi-node feedforward loops suggestive of an optimized design principle of nitrogen transcriptional regulation. This sub-circuit comprises AUXIN RESPONSE FACTOR 18 (ARF18), ARF9, DEHYDRATION-RESPONSIVE ELEMENT-BINDING PROTEIN 26 (DREB26), Arabidopsis NAC-DOMAIN CONTAINING PROTEIN 32 (ANAC032), NLP6 and NLP7 and their regulation of NITRITE REDUCTASE 1 (NIR1). Conservation and divergence of this circuit and its influence on nitrogen-dependent root system architecture were similarly assessed in tomato (Solanum lycopersicum). The specific binding sites of these factors within their respective promoters and their putative cis-regulatory architectures were identified. The direct or indirect nature of these interactions was validated in planta. The resulting models were genetically validated in varying concentrations of available nitrate by measuring the transcriptional output of the network revealing rewiring of nitrogen regulation across distinct plant lineages. 

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5. Auxin resistant 2 and short hypocotyl 2 regulate cotton fiber initiation and elongation

   https://doi.org/10.1093/plphys/kiae183  

   Jin, Fei; Zhu, Liping; Hou, Liyong; Li, Hongbin; Li, Ling; Xiao, Guanghui (March 2024, Plant Physiology)

   Abstract Auxin, a pivotal regulator of diverse plant growth processes, remains central to development. The auxin-responsive genes auxin/indole-3-acetic acids (AUX/IAAs) are indispensable for auxin signal transduction, which is achieved through intricate interactions with auxin response factors (ARFs). Despite this, the potential of AUX/IAAs to govern the development of the most fundamental biological unit, the single cell, remains unclear. In this study, we harnessed cotton (Gossypium hirsutum) fiber, a classic model for plant single-cell investigation, to determine the complexities of AUX/IAAs. Our research identified 2 pivotal AUX/IAAs, auxin resistant 2 (GhAXR2) and short hypocotyl 2 (GhSHY2), which exhibit opposite control over fiber development. Notably, suppressing GhAXR2 reduced fiber elongation, while silencing GhSHY2 fostered enhanced fiber elongation. Investigating the mechanistic intricacies, we identified specific interactions between GhAXR2 and GhSHY2 with distinct ARFs. GhAXR2's interaction with GhARF6-1 and GhARF23-2 promoted fiber cell development through direct binding to the AuxRE cis-element in the constitutive triple response 1 promoter, resulting in transcriptional inhibition. In contrast, the interaction of GhSHY2 with GhARF7-1 and GhARF19-1 exerted a negative regulatory effect, inhibiting fiber cell growth by activating the transcription of xyloglucan endotransglucosylase/hydrolase 9 and cinnamate-4-hydroxylase. Thus, our study reveals the intricate regulatory networks surrounding GhAXR2 and GhSHY2, elucidating the complex interplay of multiple ARFs in AUX/IAA-mediated fiber cell growth. This work enhances our understanding of single-cell development and has potential implications for advancing plant growth strategies and agricultural enhancements. 

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